Modeling Fmoc

I would like to modelize an Fluorenylmethyloxycarbonyl chloride (F-moc) at the end of a oligopeptide. Does anyone have any idea if it has been done before or will I have to modelize it from the begining?

where all but the OCOCl bead are S-beads. S-beads on the aromatic part would be the same as for benzene, so SC5 beads. However, you should also look for experimental partitioning data (also only for fragments of the molecule, in case you don't find data for the whole molecule) against which validate the bead type choices (see
tutorials
).

Someone affiliated with our group has done some work on Fmoc peptides recently. I will ask him to share his results. Note: the assembly of Fmoc-peptides remained tricky even with the optimized parameters for Martini 2.2.

As Pim mentioned, I've tried to parametrize Fmoc. Unfortunately, my parametrization is not perfect, and it overestimates hydrophobic interactions (experimental logP=1.4 and mine 3.6), so you will need to work a little bit on that. I have used the topology which Riccardo showed. The tricky part was to keep molecule flat - to do that I had to use two virtual sites and bending restriction potential, which requires usage of Gromacs 5. (parameterization is in a similar manner as in this paper:
aip.scitation.org/doi/10.1063/1.4937783
)

Below is the topology. For sure it is not perfect, but I think it is a good starting point. You should play more with nonbonded parameters to better reproduce logP. I used timestep 10fs.